<h2 align="center"> Welcome to the MIT BioMicro Center! </h2>

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[[File:logo.png|left]]
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* [[BioMicroCenter:News|'''News & General Information''']]
* [[BioMicroCenter:Pricing|Pricing]]
* [[BioMicroCenter:Submission|Sample Submission]]
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* [[BioMicroCenter:AboutBMC|About the BioMicro Center]]
* [[BioMicroCenter:People| Staff]]

* [[BioMicroCenter:FAQ|FAQs]]
|}
The '''MIT BioMicro Center''' is an integrated genomics core facility that provides both expertise and equipment for systems biology. The core has significant resources in sample preparation, next generation sequencing and in high throughput screening as well as bioinformatics and BioIT. The Center is a joint endeavor between the [http://biology.mit.edu Department of Biology], the [http://ki.mit.edu Koch Institute for Integrative Cancer Research] (Integrated Genomics and Bioinformatics Core (IGB)), and the [http://web.mit.edu/be Department of Biological Engineering].

{| width="100%"
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|colspan=2 align="center" style="background-color:yellow; border:1px solid purple"|
{|
|<BIG>Assisted Services </BIG>
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|align="center" style="background-color:aqua; border:1px solid black"|
{|
|<BIG> Walkup Services </BIG>
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|valign="top" align="center" style="background-color:transparent; border:1px solid black"|
{|
|width="10%" align="left"|<BIG>Sample Isolation</BIG>
* Sonication ([[BioMicroCenter:Covaris|Covaris E220/R230]])
* DNA/RNA purification ([[BioMicroCenter:Tecan_Freedom_Evo#Revvity_Chemagic_360|Chemagic360]])
* Quality Control ([[BioMicroCenter:QC|AATI Fragment Analyzer/FemtoPulse]])
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|valign="top" align="center" style="background-color:transparent; border:1px solid black"|
{|
|width="10%" align="left"|<BIG>Library Preparation</BIG>
* [[BioMicroCenter:Illumina_Library_Preparation|Short Read Sample Preparation]]
** Standard Methods for [[BioMicroCenter:DNA_LIB| *DNA* ]] [[BioMicroCenter:RNA_LIB| *RNA* ]]
** [[BioMicroCenter:FAQ#STANDARD_versus_HIGH_THROUGHPUT_LIBRARY_PREPARATION|High Throughput Methods]] for [[BioMicroCenter:DNA_HTL| *DNA* ]] [[BioMicroCenter:RNA_HTL| *RNA* ]]
* Long Read Sample Preparation ([[BioMicroCenter:NanoPore_Library_Prep|Nanopore]] and [[BioMicroCenter:PacBio_Library_Preparation|PacBio]])
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|valign="top" align="center" style="background-color:transparent; border:1px solid black"|
{|
|width="10%" align="left"|<BIG>[[BioMicroCenter:Walkup Services|Walk-up Instrumentation]]</BIG>
Includes: qPCR (LC480), Plate Readers (Varioskan/Synergy H1) BioAnalyzer, NanoDrop, Covaris, Pippin Prep Tecan/Chemagic automation MiSeq i100, 10x Chromium X
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{|
|width="10%" align="left"|<BIG>
[[BioMicroCenter:SingleCell|Single Cell]] and [[BioMicroCenter:SpTx|Spatial]]</BIG>
* 10X CHROMIUM (5'RNA, 3'RNA, ATAC, multiome) 
* 10X VISIUM (Standard, High Density) 
* ELEMENT AVITI24 (in situ prep/sequencing)
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|valign="top" align="center" style="background-color:transparent; border:1px solid black"|
{|
|width="10%" align="left"|<BIG> [[BioMicroCenter:Sequencing|Sequencing Technologies]] </BIG>
* High Yield (>1b reads) 
**[[BioMicroCenter:Illumina_Sequencing|Illumina NovaSeqX (25b,10b)]]†
* Mid Yield (250m-1b reads) 
**[[BioMicroCenter:Element Sequencing|Element AVITI24]] 
* Low Yield (1m-150m reads) 
**[[BioMicroCenter:Singular Sequencing|SingularG4]]
**[[BioMicroCenter:Illumina_Sequencing|Illumina MiSeq i100]]
* Long Read (1kb+) 
**[[BioMicroCenter:Oxford Nanopore Technologies|ONT PromethION]]
**[[BioMicroCenter:PacBio|PacBio Revio]]†
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|valign="top" align="center" style="background-color:transparent; border:1px solid black"|
{|
|width="10%" align="left"|<BIG>Automation / Library Prep</BIG>
* [[BioMicroCenter:Tecan Freedom Evo|Liquid Handlers]] ([[BioMicroCenter:Tecan_Freedom_Evo#JOHNNY_5|Tecan EVO]]
* [[BioMicroCenter:Tecan_Freedom_Evo#SPT_LABTECH_MOSQUITO_HV|SPT Mosquito]])
* [[BioMicroCenter:Covaris|Covaris E220 and R230 Focused-ultrasonicators]]
* [[BioMicroCenter:PippinPrep|Pippin Prep automated electrophoresis system]]
* [[BioMicroCenter:Oligo_Synthesis| Oligo Synthesis]]
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|valign="top" colspan=3 align="center" style="background-color: lightsalmon; border:1px solid black"|
{|
|<BIG>Informatics Services</BIG>
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{|
|width="10%" align="left"|<BIG>Data Analysis</BIG>
* [https://igb.mit.edu/ Bioinformatic Consulting]
* [[BioMicroCenter:People#INFORMATICS_LAB|Informatics Staff]]
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|valign="top" align="center" style="background-color:transparent; border:1px solid black"|
{|
|width="10%" align="left"|<BIG>BioIT/Research Computing</BIG>
* [https://koch-institute-mit.gitbook.io/mit-data-management-analysis-core/ FAIR Data Management]
* [https://igb.mit.edu/computing-resources/active-data-storage Data Storage]
* [https://igb.mit.edu/computing-resources/luria-cluster Computing on Luria]
* [https://igb.mit.edu/data-management/globus Data Transfer (Globus)]
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|valign="top" align="center" style="background-color:transparent; border:1px solid black"|
{|
|width="10%" align="left"|<BIG>Education/Training/Seminars</BIG>
* [https://igb.mit.edu/mini-courses Informatics/Computing Training Sessions]
* [[BioMicroCenter:Technology_Seminar_Series|Technology Seminar Series]]
* [http://mailman.mit.edu:/mailman/listinfo/biostuff Biostuff mailing list]
|}
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† - service will be performed in a sister core facility (Harvard, DFCI, or Broad) 
 

[https://wikis.mit.edu/confluence/display/bmc ''BMC Internal wiki'']

<h2 align="center"> CONTACT US </h2>
[http://whereis.mit.edu 68-322] 
biomicro@mit.edu 
617-715-4533

2026-03-20T15:56:27Z

Slevine: /* 10X Visium HD */

2025-09-05T19:42:01Z

Slevine:

{{BioMicroCenter}}

[[Image:FA_vs_FP.jpeg|thumb|left|400px|Visual for determining which DNA sizing instrument best suits the sample.]]

The BioMicro Center hosts several instruments to assist in quantifying nucleic acids and determining their size and purity. All samples submitted to the BioMicro Center for assisted services are routinely assayed on these instruments and they are used to monitor success of library production steps. Quality control is also a stand alone service available to researchers. Quality control instruments are currently located in 68-322.

[[Image:contaminants.jpeg|thumb|left|400px|Removal of SPRI buffer and salt allows for accurate fragment analysis.]]

All methods of quality control may fail if samples contain contaminants. The presence of SPRI bead buffer (typically PEG) or excess salts (NaCl or other) is known to quench fluorescence, ensuring that any method dependent on intercalating dye will produce unreliable results.

{|class="wikitable" border=1
! Instrument
! Description
! Measures
! Type
|-
| [[BioMicroCenter:QC#AATI_FRAGMENT_ANALYZER|AATI Fragment Analyzer]]
| Capillary Electrophoresis
| Size, Quantity
| Request via iLabs
|-
| [[BioMicroCenter:QC#AATI_FEMTO_PULSE|AATI FemtoPulse]]
| Capillary Electrophoresis
| Size, Quantity
| Request via iLabs
|-
| [[BioMicroCenter:QC#AGILENT_BIOANALYZER_2100|Agilent BioAnalyzer]]
| Microfluidics
| Size, Quantity
| Schedule via iLabs
|-
| [[BioMicroCenter:QC#NanoDrop_ND-1000|Nanodrop]]
| Absorbance
| Purity, Quantity
| Walk-up
|-
| [[BioMicroCenter:Varioskan|Varioskan:Picogreen]]
| Absorbance
| Quantity
| Schedule via iLabs
|-
| [[BioMicroCenter:Varioskan|Varioskan:Synergy_H1]]
| Absorbance
| Quantity, Purity
| Schedule via iLabs
|}
 
.
== AATI FRAGMENT ANALYZER ==
{|
|- style="vertical-align: top;"
|style="width: 400px;"|
{| class="wikitable" border=1
!Service
!AATI FRAGMENT ANALYZER
|-
|INPUT || 5uL for standard 2uL/well for preload
|-
|SUBMISSION || MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=4110 ilabs] External - [[BioMicroCenter:Forms|form]] Preloaded rows must be in semiskirted plates from the BioMicro Center (or equivalent).
|-
|UNIT || Samples or preloaded rows
|-
|TURN AROUND || Typically < 1 business day
|-
|SAMPLE SUBMISSION || 9a-4:30p normal weekdays. Samples brought by after 4:30p must be accompanied by cookies.
|-
|DONATED BY || Department of Biology
|}
|
The [[BioMicroCenter:Advanced_analytical_Fragment_analyzer|Advanced Analytical Fragment Analyzer (FA)]] is a highly efficient and accurate fluorescence-based electrophoresis instrument used to size and quantify DNA and RNA. It is faster and more cost effective than the BioAnalyzer2100, and can handle unsupervised runs of up to 192 samples. Each run takes ~60 minutes and 2 μL of sample. Users may submit any volume of sample with the expectation that if there is less than 2 μL, the samples will be diluted. To save money and submit a larger quantity of samples, users may come into the BMC and obtain a special 96 well plate or plates. For mass submission, 2 μL must be put into each sample well row by row. There is a way to submit rows in iLabs, but please remember to come and get special plates from the BMC to do mass submission. 

The Fragment analyzer was purchased in 2012 and upgraded to handle 48 samples in a batch in 2017. Fragment analyzer reports a "RIN eQuivalent Number (RQN) instead of RIN.
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[[Image:FA.jpg|right]]
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|colspan = "2"|
{| class="wikitable" border=1
! Assay
! Sizing Range
! Concentration Range
|-
|High Sensitivity DNA
|50bp - 5kbp
|Fragment: 5pg-1ng/uL Smear: 50pg-5ng/uL
|-
|Nano RNA
|50bp - 5kbp

|}
|
|}

== AATI FEMTO PULSE ==
{|
|- style="vertical-align: top;"
|style="width: 400px;"|
{| class="wikitable" border=1
!Service
!AATI FEMTO PULSE
|-
|INPUT || 5uL for standard 2uL/well for preload
|-
|SUBMISSION || MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=4110 ilabs] -- External - [[BioMicroCenter:Forms|form]] Preloaded rows must be in semiskirted plates from the BioMicro Center (or equivalent).
|-
|UNIT || Samples or preloaded rows
|-
|TURN AROUND || Typically < 1 business day
|-
|DONATED BY || MIT CEHS
|}
|
The [[BioMicroCenter:FemtoPulse|FEMTO Pulse (FP)]] is an instrument that provides a remarkable upgrade over the existing FA and Agilent BioAnalyzer2100 technologies that have been available for many years. While still an instrument to analyze the lengths of nucleic acids, the FEMTO Pulse adds a pulse filed generator to allow the separation and characterization of significantly longer molecules, out to 200,000 base pairs. Additionally, the FP has significantly improved optics that allow approximately two orders of magnitude of additional sensitivity. Where the FA bottoms out a sensitivity of 2-3pg/ul, the FP has nearly 100x improved sensitivity which may enable this instrument to directly observe molecular reactions without the need for amplification or modification with radioactive nucleotides. 

The FEMTO Pulse runs 12 samples at a time using 2ul of material. Each run takes ~90 minutes to run. It is *not* a replacement for the Fragment Analyzer and is optimized for very low inputs or very long samples. 
|
[[image:BMC_FP_instrument.jpeg|right]]
|-
|colspan = "2"|
{| class="wikitable" border=1
! Assay
! Sizing Range
! Concentration Range
|-
|NGS DNA
|50bp - 5kbp
|Smear: 2.5-500pg/uL Fragment 50fg-5pg/uL
|-
|Genomic DNA
|2kbp - 160kbp
|Smear: 2.5 - 500pg/uL
|-
|Femto RNA
|50bp - 5kbp
|2.5pg-500pg/uL
|}
|
|}

== AGILENT BIOANALYZER 2100 ==
{|
|- style="vertical-align: top;"
|style="width: 300px;"|
{| class="wikitable" border=1
!Service
!Agilent BioAnalyzer
|-
|SERVICE || WALKUP
|-
|INPUT || 1uL/well
|-
|SCHEDULE || [https://mit.ilabsolutions.com/equipment/show/265040 MIT iLabs]
|-
|UNIT || Per Chip
|-
|RUN TIME || ~1 hour
|}
|
The Agilent 2100 BioAnalyzer is a microfluidics device that performs size determination and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to perform flow cytometry on small numbers of cells. Samples can be run on the BioAnalyzer by individual users; the BioMicro Center does not currently accept sample submissions to be run on the BioAnalyzer by BMC staff. 

The BioAnalyzer can be scheduled for usage on iLabs after the user has received training by emailing bmcwetlab@mit.edu (Core Labs only please). This service will be discontinued if we find the machine is abused. Once you are trained in the use of the BioAnalyzer you are welcome to sign up for usage on ilabs.
|
[[Image:Presentation4.jpg|right|200px]]
|-
|colspan="2"|
{| class="wikitable" border=1
! Assay !! Sizing Range !! Concentration Range
|-
|High Sensitivity DNA ||50bp - 7kbp || 5-500pg/ul
|-
|RNA Nano || 25bp - 5kbp || 25-500 ng/ul total RNA
|-
|RNA Pico || 25bp - 5kbp || 0.05-5 ng/ul total RNA
|-
|small RNA || 6bp-150bp || 0.05-2 ng/ul smallRNAs
|-
|High Sensitivity Protein || 10kD-250kD || 0.3ng/ul
|-
|}
Note: not all assays are listed.
|
|}

== NanoDrop ND-1000 ==
{| align=left
|- style="vertical-align: top;"
|style="width: 300px;"|
{| class="wikitable" border=1
! Instrument || NANODROP
|-
| TYPE || WALKUP
|-
| PRICING || NO CHARGE
|-
| WAVELENGTH || 220-750nm
|-
| MIN CONC || ~10ng/uL
|-
| SIGNUP || No Signup Necessary.
|}
|
The NanoDrop ND-1000 is a full-spectrum (220 - 750nm) spectrophotometer that measures 1ul samples without the use of cuvettes or the need for dilution. The NanoDrop ND-1000 is located at the BMC, building 68-322 and is FREE for [[BioMicroCenter:CoreDeps|core department]] use
|
[[Image:Nd-1000.jpg|right|200px]]
|}